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VirusMINT: a viral protein interaction database

A. Chatr-aryamontri, A. Ceol, D. Peluso, A. Nardozza, S. Panni, F. Sacco, M. Tinti, A. Smolyar, L. Castagnoli, M. Vidal, M. E. Cusick, G. Cesareni
2009 Nucleic Acids Research  
The VirusMINT database (http://mint.bio.uniroma2. it/virusmint/) aims at collecting all protein interactions between viral and human proteins reported in the literature.  ...  VirusMINT currently stores over 5000 interactions involving more than 490 unique viral proteins from more than 110 different viral strains.  ...  Interactions involving proteins obtained from the processing of the same viral polyprotein are considered as distinct in VirusMINT. Each interaction is also assigned a confidence score (10) .  ... 
doi:10.1093/nar/gkn739 pmid:18974184 pmcid:PMC2686573 fatcat:5i3kju2xx5esnjonkbmzt5zoqe

VirusMentha: a new resource for virus-host protein interactions

Alberto Calderone, Luana Licata, Gianni Cesareni
2014 Nucleic Acids Research  
In order to provide a general overview of such interactions, a few years ago we developed VirusMINT.  ...  Viral proteins target host proteins and either form new complexes or modulate the formation of functional host complexes.  ...  Although this information can in principle be extracted from generic protein interaction databases, 5 years ago we developed VirusMINT (3), a protein-protein interaction (PPI) database focused on viral  ... 
doi:10.1093/nar/gku830 pmid:25217587 pmcid:PMC4384001 fatcat:vimbvvqkxjdkpl2ksi3w5c6btm

VPDB: Viral Protein Structural Database

Om Prakash Sharma, Ankush Jadhav, Afzal Hussain, Muthuvel Suresh Kumar
2011 Bioinformation  
Database Volume 6(8) ISSN 0973-2063 (online) 0973-8894 (print) Bioinformation 6(8): 324-326 (2011) 324 Abstract: Viral Protein Database is an interactive database for three dimensional viral proteins.  ...  Interactivity has been enhanced by using Jmol, WebMol and Strap to visualize the viral protein molecular structure.  ...  VirusMINT VirusMINT is a database which shows interaction between human and viral proteins. http://mint.bio.uniroma2.it/virusmint/Welcome.do VIDA VIDA database contains a complete collection of homologous  ... 
doi:10.6026/97320630006324 pmid:21769196 pmcid:PMC3134783 fatcat:tb7fmcf6cbgoppbmh52hs62vsm

Virus interactions with human signal transduction pathways

Zhongming Zhao, Junfeng Xia, Oznur Tastan, Irtisha Singh, Meghana Kshirsagar, Jaime Carbonell, Judith Klein Seetharaman
2011 International Journal of Computational Biology and Drug Design  
Viruses depend on their hosts at every stage of their life cycles and must therefore communicate with them via Protein-Protein Interactions (PPIs).  ...  We find evidence supporting the hypothesis that viruses often interact with different proteins depending on the targeted pathway.  ...  The VirusMINT database contains PPI data for 557 proteins and 149 different viral strains.  ... 
doi:10.1504/ijcbdd.2011.038658 pmid:21339552 pmcid:PMC3407688 fatcat:hxj67avizrbudaymttqykg4r7y

Comparative Interactome of HIV-1 Tat and Human T Lymphotropic Virus Type-1 Tax and the Cellular Transcriptional Machinery

Charlotte Vandermeulen, Léon-Juvenal Hajingabo, Jean-Claude Twizere
2015 AIDS Research and Human Retroviruses  
CREB/ATF factors (ATF4, CEBBP, KAT2B), chromatin modifying enzymes (HDAC1 and MBD2) and cyclin T1, a member of the positive transcription elongation factor pTEF-B.  ...  The results are collected in various databases including HIV-1 Human Interaction Database (ref), VirusMINT and VirHostNet.  ...  between the viral and the host proteins.  ... 
doi:10.1089/aid.2014.0377 pmid:26599333 fatcat:uuhqnhwqjfcnfbmbqmffjt32by

Global landscape of HIV–human protein complexes

Stefanie Jäger, Peter Cimermancic, Natali Gulbahce, Jeffrey R. Johnson, Kathryn E. McGovern, Starlynn C. Clarke, Michael Shales, Gaelle Mercenne, Lars Pache, Kathy Li, Hilda Hernandez, Gwendolyn M. Jang (+25 others)
2011 Nature  
Black edges correspond to interactions between host factors (289) that were obtained from publicly available databases; dashed edges correspond to interactions also found in VirusMint 14 . 29 .  ...  We also introduced 289 interactions between human proteins (black edges) derived from several databases 19, 20 (Supplementary Data 9) .  ...  Briefly, affinity tagging and purification was carried out as previously described 2 and the protein samples were analysed on a Thermo Scientific LTQ Orbitrap XL mass spectrometer.  ... 
doi:10.1038/nature10719 pmid:22190034 pmcid:PMC3310911 fatcat:zzax6urzhndlhdf3whdvec7coe

Prediction of Interactions between Viral and Host Proteins Using Supervised Machine Learning Methods

Ranjan Kumar Barman, Sudipto Saha, Santasabuj Das, Dinesh Gupta
2014 PLoS ONE  
Viral-host protein-protein interaction plays a vital role in pathogenesis, since it defines viral infection of the host and regulation of the host proteins.  ...  viral-host PPIs from VirusMINT.  ...  The viral-host PPIs dataset were obtained from VirusMINT, a viral protein interaction database [17] .  ... 
doi:10.1371/journal.pone.0112034 pmid:25375323 pmcid:PMC4223108 fatcat:4zthu2s4ybem3kojqirn4enrx4

PROGRESS IN COMPUTATIONAL STUDIES OF HOST–PATHOGEN INTERACTIONS

HUFENG ZHOU, JINGJING JIN, LIMSOON WONG
2013 Journal of Bioinformatics and Computational Biology  
of hostÀpathogen proteinÀ protein interactions; basic principles revealed from hostÀpathogen interactions; and database and software tools for hostÀpathogen interaction data collection, integration and  ...  as a pair of homologous proteins descend from the same ancestral pair of interacting proteins and is expected to inherit the structure and function and, thus, interactions of the ancestral proteins.  ...  This project was supported in part by an NGS scholarship and a Singapore Ministry of Education Tier-2 grant MOE2009-T2-2-004.  ... 
doi:10.1142/s0219720012300018 pmid:23600809 fatcat:acmp22pmyfhpla3sst53lsx3qa

GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data

Marie E Fahey, Melanie J Bennett, Cathal Mahon, Stefanie Jäger, Lars Pache, Dhiraj Kumar, Alex Shapiro, Kanury Rao, Sumit K Chanda, Charles S Craik, Alan D Frankel, Nevan J Krogan
2011 BMC Bioinformatics  
Because these host-pathogen interactions are extensive and interactions between human proteins are found within many different databases, it is difficult to generate integrated HIV-human interaction networks  ...  between human proteins derived from publicly-available databases, including MINT, BioGRID and HPRD.  ...  N.J.K. is a Keck Young Investigator and Searle Scholar.  ... 
doi:10.1186/1471-2105-12-298 pmid:21777475 pmcid:PMC3213248 fatcat:cx2my7mg2jgcpiidepzj7u4a2y

Amino acids special issue 'Protein interactions in the virus–host relationship'

Alessandro Marcello
2009 Amino Acids  
Gianni Cesareni and his group developed a database, VirusMINT, that stores in a structured format most of the published interactions between viral and host proteome (Carducci et al. 2010) .  ...  Hence, understanding viral protein functions and their interactions with host proteins is a prerequisite for the rational development of antiviral compounds.  ... 
doi:10.1007/s00726-009-0441-6 pmid:20020162 fatcat:cpyocnhxhjhenk7wqrg6ualyyq

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

Thibaut Guirimand, Stéphane Delmotte, Vincent Navratil
2014 Nucleic Acids Research  
VirHostNet release 2.0 (http://virhostnet.prabi.fr) is a knowledgebase dedicated to the network-based exploration of virus-host protein-protein interactions.  ...  The new interface of VirHostNet 2.0 is based on Cytoscape web library and provides a user-friendly access to the most complete and accurate resource of virus-virus and virus-host protein-protein interactions  ...  It also provides a useful taxonomy summary of the protein interaction network (the number of viral and host proteins, the number of VH, VV, HH ppi).  ... 
doi:10.1093/nar/gku1121 pmid:25392406 pmcid:PMC4383936 fatcat:hhyashqdsjdylbghnmvdtqbvxi

Analysis of Virus-Host Interactomes through a network-centric approach [article]

Pietro Hiram Guzzi, Giuseppe Tradigo, Pierangelo Veltri
2020 bioRxiv   pre-print
Mechanisms of infections of viruses are mediated by Protein-protein interactions (PPIs).  ...  In this work, we propose a methodology to model and analyse host-pathogen interactions and a supporting tool able to analyse such data.  ...  Host-Pathogen Data The VirusMINT database [8] is derived from the MINT database and it is based on the collection of protein interaction data from literature.  ... 
doi:10.1101/2020.06.30.179945 fatcat:eanctmvmqngu3lpug2taxfzhoy

Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research

Deepak Sharma, Pragya Priyadarshini, Sudhanshu Vrati, S. P. Goff
2014 Journal of Virology  
RNA [shRNA]/microRNA [miRNA] studies, RNA folding, protein-protein interaction, structural analysis, and phylotyping and genotyping) will definitely aid the development of effective drugs and vaccines  ...  The availability of more than 100 Web servers and databases embracing all or specific viruses (for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic  ...  Access b URL (reference) VirusMINT Hosts interactions between viral and human proteins 16.5 e W http://mint.bio.uniroma2.it/virusmint/ (90) Virus-PLoc Prediction of subcellular location of viral  ... 
doi:10.1128/jvi.02027-14 pmid:25428870 pmcid:PMC4300767 fatcat:2qgddtkbzzfztiyymbwksd7lvq

Bioinformatics and database resources in hepatology

Andreas Teufel
2015 Journal of Hepatology  
The VirusMINT database provides a comprehensive summary of protein interactions between viral and human proteins reported in the literature.  ...  VirusMINT A detailed understanding of the molecular interactions between host physiology and viral infection will certainly be a major aid in targeting viral hepatitis.  ... 
doi:10.1016/j.jhep.2014.10.036 pmid:25450718 fatcat:2zt6jzlclnce7bumevj3r6752u

Interactome of the hepatitis C virus: Literature mining with ANDSystem

Olga V. Saik, Timofey V. Ivanisenko, Pavel S. Demenkov, Vladimir A. Ivanisenko
2016 Virus Research  
Acknowledgments Extension of structure of the ANDCell database for storing data about interspecies interactions (HCV interactome) was conducted under financial support of FP7 EU grant SysPatho No. 260429  ...  The development of new semantic templates for the automated text analysis and extraction of information about HCV-host interactions was performed with the financial support by the VI.61.1.2 project.  ...  The VirusMINT database (http://mint.bio. uniroma2.it/virusmint/Welcome.do) possesses information on 394 interactions between proteins of HCV and host proteins extracted from the literature.  ... 
doi:10.1016/j.virusres.2015.12.003 pmid:26673098 fatcat:xhdcj4qjtbachee4qjbt2jg27u
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